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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF PROTEIN Z COMPLEXED WITH PROTEIN Z-DEPENDENT INHIBITOR

Authors :   A. Zhou

Date :   28 Oct 08 (Deposition) - 30 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Pz, Zpi, Complex, Serpin, Protease Inhibitor, Protease, Glycoprotein, Secreted, Serine Protease Inhibitor, Blood Coagulation, Cleavage On Pair Of Basic Residues, Egf-Like Domain, Gamma-Carboxyglutamic Acid, Hydroxylation, Serine Protease Homolog, Hydrolase Inhibitor- Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Wei, Y. Yan, R. W. Carrell, A. Zhou
Crystal Structure Of Protein Z-Dependent Inhibitor Complex Shows How Protein Z Functions As A Cofactor In The Membrane Inhibition Of Factor X.
Blood 2009
PubMed-ID: 19528533 | Reference-DOI: 10.1182/BLOOD-2009-04-210021

Molecule 1 - PROTEIN Z-DEPENDENT PROTEASE INHIBITOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSUMO3
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	EGF2 AND PROTEASE DOMAIN
	Gene	:	SERPINA10, UNQ707/PRO1358, ZPI
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PZ-DEPENDENT PROTEASE INHIBITOR, PZI, SERPIN A10

Molecule 2 - VITAMIN K-DEPENDENT PROTEIN Z
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell	:	HEK293 CELLS
	Expression System Plasmid	:	PCEP4
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 125-400
	Gene	:	PROZ, PZ
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	FLC	1	Ligand/Ion	CITRATE ANION
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:72 , TYR A:325 , GLU A:326 , HOH A:429 , HOH A:441	BINDING SITE FOR RESIDUE CL A 1
2	AC2	SOFTWARE	SER A:64 , ARG A:67 , ARG B:212	BINDING SITE FOR RESIDUE EDO A 424
3	AC3	SOFTWARE	GLN A:102 , ARG A:337 , ARG A:338 , SER A:341 , ARG A:364 , LEU A:423	BINDING SITE FOR RESIDUE FLC A 425
4	AC4	SOFTWARE	HOH B:5 , ASN B:193	BINDING SITE FOR RESIDUE NAG B 1

Asymmetric/Biological Unit

No.	Residues
1	B:89	-	B:101
2	B:97	-	B:110
3	B:112	-	B:125
4	B:131	-	B:233
5	B:133	-	B:241
6	B:163	-	B:179
7	B:287	-	B:301

Asymmetric/Biological Unit

No.	Residues
1	Arg A:354	-	Asn A:355
2	Cys B:233	-	Pro B:234

Asymmetric/Biological Unit (10, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_020326	S	61	G	ZPI_HUMAN	Polymorphism	941591	A	S	40	G
02	UniProt	VAR_038833	G	139	R	ZPI_HUMAN	Polymorphism	56137907	A	G	118	R
03	UniProt	VAR_051940	L	158	Q	ZPI_HUMAN	Polymorphism	2232699	A	L	137	Q
04	UniProt	VAR_020327	T	161	S	ZPI_HUMAN	Polymorphism	2232700	A	T	140	S
05	UniProt	VAR_051941	R	196	H	ZPI_HUMAN	Polymorphism	2232701	A	R	175	H
06	UniProt	VAR_038834	G	271	S	ZPI_HUMAN	Polymorphism	2232708	A	G	250	S
07	UniProt	VAR_013125	R	295	H	PROZ_HUMAN	Polymorphism	3024772	B	R	255	H
08	UniProt	VAR_038835	Q	384	P	ZPI_HUMAN	Polymorphism	---	A	Q	363	P
09	UniProt	VAR_051942	Q	384	R	ZPI_HUMAN	Polymorphism	2232710	A	Q	363	R
10	UniProt	VAR_070192	F	420	L	ZPI_HUMAN	Polymorphism	546304706	A	F	399	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EGF_2	PS01186	EGF-like domain signature 2.	PROZ_HUMAN	111-122 150-165	1	- B:110-125
2	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	PROZ_HUMAN	175-400	1	B:135-360

(no "Exon" information available for 3F1S)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:385
 aligned with ZPI_HUMAN | Q9UK55 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:385
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439     
            ZPI_HUMAN    60 ASEEEKAWLMASRQQLAKETSNFGFSLLRKISMRHDGNMVFSPFGMSLAMTGLMLGATGPTETQIKRGLHLQALKPTKPGLLPSLFKGLRETLSRNLELGLTQGSFAFIHKDFDVKETFFNLSKRYFDTECVPMNFRNASQAKRLMNHYINKETRGKIPKLFDEINPETKLILVDYILFKGKWLTPFDPVFTEVDTFHLDKYKTIKVPMMYGAGKFASTFDKNFRCHVLKLPYQGNATMLVVLMEKMGDHLALEDYLTTDLVETWLRNMKTRNMEVFFPKFKLDQKYEMHELLRQMGIRRIFSPFADLSELSATGRNLQVSRVLQRTVIEVDERGTEAVAGILSEITAYSMPPVIKVDRPFHFMIYEETSGMLLFLGRVVNPTLL 444
               SCOP domains d3f1sa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3f1sA02 A:221-318,A:372-423 Alpha-1-antitrypsin, domain 1                                         -----------------------------------------------------3f1sA02 A:221-318,A:372-423                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh....hhhhhhhhhhh..........hhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh................eeeeeeeeee.......hhhhheeeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeeee...eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh..................eeeeeeeeee......................eee....eeeeeee.....eeeeeee...... Sec.struct. author
             SAPs(SNPs) (1) -G-----------------------------------------------------------------------------R------------------Q--S----------------------------------H--------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------------P-----------------------------------L------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f1s A  39 ASEEEKAWLMASRQQLAKETSNFGFSLLRKISMRHDGNMVFSPFGMSLAMTGLMLGATGPTETQIKRGLHLQALKPTKPGLLPSLFKGLRETLSRNLELGLTQGSFAFIHKDFDVKETFFNLSKRYFDTECVPMNFRNASQAKRLMNHYINKETRGKIPKLFDEINPETKLILVDYILFKGKWLTPFDPVFTEVDTFHLDKYKTIKVPMMYGAGKFASTFDKNFRCHVLKLPYQGNATMLVVLMEKMGDHLALEDYLTTDLVETWLRNMKTRNMEVFFPKFKLDQKYEMHELLRQMGIRRIFSPFADLSELSATGRNLQVSRVLQRTVIEVDERGTEAVAGILSEITAYSMPPVIKVDRPFHFMIYEETSGMLLFLGRVVNPTLL 423
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with PROZ_HUMAN | P22891 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:275
                                                                                                                                                                                                                                                                                                           400 
                                   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   | 
           PROZ_HUMAN   127 NECHPERTDGCQHFCLPGQESYTCSCAQGYRLGEDHKQCVPHDQCACGVLTSEKRAPDLQDLPWQVKLTNSEGKDFCGGVIIRENFVLTTAKCSLLHRNITVKTYFNRTSQDPLMIKITHVHVHMRYDADAGENDLSLLELEWPIQCPGAGLPVCTPEKDFAEHLLIPRTRGLLSGWARNGTDLGNSLTTRPVTLVEGEECGQVLNVTVTTRTYCERSSVAAMHWMDGSVVTREHRGSWFLTGVLGSQPVGGQAHMVLVTKVSRYSLWFKQIMN-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f1sB01 B:87-137 Laminin                           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................eee......eee...........--------....eeeee.....eeeeeeeee..eeeehhhhhh.....eeee....-....eeeeeeeeee.............eeeee................hhhhhhhh......eeeee....-------.eeeeeeeehhhhhhhhhh......eeeee...hhhhh....eeeee....eeeeeee...hhhhh..eeeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------EGF_2           ---------TRYPSIN_DOM  PDB: B:135-360 UniProt: 175-400                                                                                                                                                                                      - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f1s B  87 NECHPERTDGCQHFCLPGQESYTCSCAQGYRLGEDHKQCVPHDQCACGVLTS--------DLPWQVKLTNSEGKDFCGGVIIRENFVLTTAKCSLLHRNITVKTYFNR-SQDPLMIKITHVHVHMRYDADAGENDLSLLELEWPIQCPGAGLPVCTPEKDFAEHLLIPRTRGLLSGWARN-------LTTRPVTLVEGEECGQVLNVTVTTRTYCERSSVAAMHWMDGSVVTREHRGSWFLTGVLGSQPVGGQAHMVLVTKVSRYSLWFKQIMNA 361
                                    96       106       116       126       136 |       -|      156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356     
                                                                             138      147                                            194 |                                                                   266     274                                                                                       
                                                                                                                                       196

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: automated matches (20)

Protein domain: automated matches (20)

Human (Homo sapiens) [TaxId: 9606] (9)

d3f1sa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Laminin (270)

Homologous Superfamily: Laminin (263)

Human (Homo sapiens) (195)

3f1sB01

B:87-137

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

3f1sA02

A:221-318,A:372-423

(no "Pfam Domain" information available for 3F1S)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ZPI_HUMAN | Q9UK55)

molecular function
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0008218	bioluminescence	The production of light by certain enzyme-catalyzed reactions in cells.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0060046	regulation of acrosome reaction	Any process that modulates the frequency, rate or extent of the acrosome reaction.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Chain B (PROZ_HUMAN | P22891)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0017187	peptidyl-glutamic acid carboxylation	The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006465	signal peptide processing	The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:354 - Asn A:355	[ RasMol ]
		Cys B:233 - Pro B:234	[ RasMol ]

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	3f1s
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	ZPI_HUMAN \| Q9UK55
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	PROZ_HUMAN \| P22891	:	3h5c
	ZPI_HUMAN \| Q9UK55	:	3h5c 4afx 4aju

(no "Related Entries Specified in the PDB File" available for 3F1S)

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (7, 7)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (10, 10)

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